The Substitution Game
by Lady Calipso
Summary: When Annabelle McCrane notices her boss acting very strangely, a man called the Doctor comes in to investigate. Together they enter the boss's room only to find that he is missing.
1. Chapter 1

On a pleasant Florida afternoon, Annabelle McCrane was enjoying lunch on a park bench just outside of her workplace. As she took another bite of her sandwich, she noticed a tall man in a slightly unusual outfit running to and fro as if he was searching for something. She assumed that it was nothing to worry about and continued eating her lunch. A few minutes later the strange man approached the area where Annabelle was sitting and kept searching. She still paid no heed to the stranger until he attempted to climb the tree that was shading her.

"Can I help you?" Annabelle asked.

"Why yes," the man panted, "Have you seen my sonic screwdriver?"

"Your what?" replied Annabelle as she looked at the man. He was wearing a brown coat, a plain collared white shirt, a brown hat, and an unusually long colorful scarf.

"My sonic screwdriver," he repeated. "It's a device that makes a whirring sound and opens doors. Doesn't work on wood though."

"What does it look like?" said Annabelle as she looked around.

"Well it's silver with a red and black head," he answered.

"Does it look like something a doctor would use?" she asked. The man nodded then Annabelle pointed to an object beside a tree, "Would that be your sonic screwdriver over there?"

"Indeed it is," the man said in a surprised fashion. "Thank you very much." He retrieved his sonic screwdriver then asked, "By the way, what is today's date?"

"It's November 23, 2012."

"Ah the year the Mayan Calendar ends. Thank you." He turned and proceeded to walk towards the nearby buildings.

Annabelle was fascinated by the stranger, yet she was not willing to let him depart until she learned more about him. So she set aside her lunch and stood up to officially meet the stranger.

"I never did get your name sir," Annabelle said.

"That's because I never gave it," he replied as he turned to face Annabelle.

"Well," smiled Annabelle, "My name is Annabelle McCrane, but most people call me Annie. Who might you be?"

"I'm called the Doctor," the man replied as he reached to shake Annie's hand. "It is a pleasure to meet you, Ms. McCrane." As they shook hands, Annie saw that the Doctor took a particular notice to her necklace with several charms. "Well I must be off. Good day." With that he briefly lifted his hat from his head and proceeded to walk to the buildings. "Nice necklace." he called.

Annie placed her fingers on the pendant of the chain and watched as he walked away. "Thanks." she replied softly. _What a strange man that Doctor is._ Annie thought, _I would like to get to know him better, but I suppose I should wait for another chance to talk to him. Besides I need to get back to work._ She collected her lunch and went back to her work place still hoping she might encounter the Doctor again.

* * *

Annie went back to her job as secretary for the executive of Burrdey Food Bank, but she noticed something strange about her boss. When she resumed her assigned tasks, her executive stormed out of his office.

"Where have you been for the last hour?" he snapped at her.

"I was on lunch break," Annie replied in a confused manner.

"Lunch break?" he exclaimed, "Since when did I give you a lunch break?"

"Since my first day," Annie said, still confused, "You've allowed me to go on lunch break from eleven o'clock until noon. It has always been like that since I first started working here, sir." Annie looked at him while trying to understand the situation. "Are you alright, sir?" she asked after a moment, "You seem to be acting strangely this afternoon."

"I'm fine. Get back to your work," he barked and retreated back to his office.

 _That was very strange._ Annie thought to herself, "He has never been like that before. How did he forget my lunch break? Something is not right."


	2. Chapter 2

An hour had passed since Annie had returned from her break. She sat at her desk, her blonded hair in a bun, and resumed work. As she was typing into her computer, the Doctor showed up with a metal dog in tow.

"Hello, Doctor, nice to see you again," she said slightly surprised, "What brings you here?"

"Hello, Annie, K-9 here has detected a strange signal coming from this building. I'm here to investigate. Oh, by the way, this is my dog, K-9," the Doctor said as he pointed towards the robot.

Annie leaned over her desk and looked at the dog as if she was a shy child meeting a new friend.

"The signal seems to be coming from the room straight ahead, Master," stated K-9.

"That's the Executive's office," she said taking her seat again, "What kind of signal is coming from there?"

"A signal that does not belong to Earth," the Doctor replied.

"You mean it's alien, as in extra-terrestrial?" said Annie

"You may put it that way if you like," the doctor answered, "Tell me, Annie, has your boss been acting strangely recently?"

"Yes," Annie stated, "He has been acting differently this afternoon. When I came back from my lunch break, he demanded to know why I was gone. It seemed like he forgot that I have a lunch break, but that's not the only thing. As he was yelling, I smelled this weird odor, which smelled like iron, but I…"

"That explains it!" the Doctor interrupted, "Annie, I have a feeling that whoever is in that office, is not your boss."

"What do you mean?" said Annie, "Do you mean that my boss is now an alien? You can't expect me to believe that."

"I mean that something is posing as your boss. Most likely that something did not come from Earth," said the Doctor.

"Extra-terrestrials?" stated a shocked Annie, "I find that hard to believe, but you do have a sonic screwdriver and a robotic dog. So why not."

"Well that's good. Anyway, I'm going to need to see the executive so I can figure out what's going on."

"Alright, I'll give him a buzz, see what he's doing," she then pushed a button on a speaker and proceeded to talk into it. "Mr. Anderson. There is a man out here who wishes to see you."

"Tell him I do not wish to be disturbed," said a voice from the speaker.

The Doctor got closer to the speaker and said, "It will only take a few minutes."

"No! I am very busy at the moment. Please come back at a different time. Good day," replied the voice.

"Good day," said the Doctor sounding defeated. "I need to get in that office. Something is definitely not right. Come along K9."

"I'm coming too," declared Annie.

"No, it could be dangerous," said the Doctor.

"So? You may need my help in there. After all I am his secretary."

"Fine, but don't say I didn't warn you."

The Doctor, Annie, and K-9 quietly headed towards the executive's office. The Doctor pulled out his sonic screwdriver, unlocked the door, and slowly opened it. The three of them entered the office and found the office empty.

"Where did he go?" said a perplexed Annie, "Mr. Anderson? How could he have left his office without us seeing him? There aren't any exits in this room."

"Perhaps he was teleported," stated K-9.

"Perhaps indeed," said the Doctor as he looked around the office. He then picked up a strange looking device. "K-9, is this the source of the signal?"

"Affirmative, Master.," said K-9.

"Can you tell me more about this device?" asked the Doctor

"Affirmative. Scan suggests device is used for communication. Device is known to be used by Zygons."

"Zygons, just as I thought. A Zygon must have taken my sonic screwdriver earlier and now one is posing as Mr. Anderson."

"Zygons? What are those?" Annie inquired.

"Zygons: a metamorphic species that can pose as any living being," K-9 defined.

"It would appear that a Zygon has taken your boss and has been impersonating him for at least a couple of hours," the Doctor added.

"Why would a Zygon want to do that and what does it have do with Mr. Anderson?" Annie questioned.

"I'm not quite sure. Perhaps they need his position for their plan, whatever it may be."

"Where would they have taken him?"

"They would have taken him to their ship I'd imagine."

"Is there a chance he may still be alive?"

"Oh, quite certainly. The Zygons need living specimens in order to take their form. The question is where is the ship that he is being held in? K-9, are you able to identify the receiving end of the signal?"

"Negative. The signal can only be traced if it is active."

"Alright then. K-9, I'm going to send a message through this device. I want you to find out where the signal goes," with that the Doctor started pushing buttons on the communication device. Then the device made a strange noise.

"The signal is being directed towards a ship located approximately 38.7852 kilometers to the west," K-9 responded

"That would put it near Lake Apopka," Annie stated.

"Not near in," the Doctor corrected

"What do you mean?"

"Well if you had a spaceship from another world, wouldn't you want to hide it?" he said as he began walking towards the door. When he was walking, a small cylindrical object bathed in an unnatural light appeared next to Annie. Within seconds the object rapidly released a whitish gas.

"Nerve gas!" he exclaimed, "Annie don't inhale it." but his words were of no effect as Annie was already coughing violently and on the verge of passing out.

Within moments Annie was out and the Doctor felt faint while trying to combat the fumes. Then two large beams of light appeared in the room. Out of those beams two Zygons materialized. They were tall, red, and covered with suckers. They had a strange, earthy smell to them. When they fully materialized, one of them closed the nerve gas canister while the other checked to make sure that they would not meet resistance. K-9 detected them and fired laser beams at the intruders to stun them; the Zygons had a type of shielding on them, so the beams were of no effect. They took no notice of K-9. Instead they made sure the room was clear, then took the Doctor.


	3. Chapter 3

_Children cheered and clamored while they watched a young girl swing her fists at a boy who was taunting her._

" _Come on, is that all you can do?", "You fight like a girl,", the boy jeered, "You're never getting your mom's bracelet back." The boy had taken the girl's bracelet and used it to tease her._

 _"Give it back," the girl pleaded as she reached and swung at him, "that's my mom's."_

 _"What's going on here!" a large woman yelled._

 _The boy put the bracelet in his pocket as the woman stomped towards them. "She hit me and called me names." he tattled._

" _Annabel! What do you have to say for yourself?" the woman roared._

" _He took my bracelet," Annie cried_

" _I did not!" he retorted_

" _Annie, you know better than to fib," the woman said, "Johnny would never take your bracelet. Come on, let's go think about what you did." with that she led Annie toward her office. Annie brushed against Johnny as she passed by._

" _Annie, no one will ever adopt you if you keep misbehaving like this. Now I want you to stand in the corner and think about what you did," the woman told her. Annie silently obeyed then fiddled with her mother's bracelet which she took back from Johnny when she brushed past._

* * *

"Annie?", "Annie?"

Annie woke up to find K-9 beside her calling her name. "K-9?" she asked wearily, "Wha… What happened? Where's the Doctor?"

"The Zygons placed a nerve gas cannister. The nerve gas rendered you and Master unconscious. I fired a laser beam at them, but it did not affect them. They took Master," K-9 replied.

"Do you know where they took him?" Annie inquired.

"It is logical to assume that they took him to their ship, which has been determined to be located in Lake Apopka."

"Well, if that's where they took the Doctor, that must be where they took Mr. Anderson. Come on K-9. Let's go get your master and Mr. Anderson," Annie went to collect her things as the metallic dog followed. " _hmm_ K-9, do Zygons have any fears or weaknesses?"

"Affirmative. Zygons are known to have an innate fear of fire," Annie got to her car, placed K-9 inside as well, then drove to go rescue Mr. Anderson and the Doctor.

"The Time lord is acquired," said a gruff voice.

"Good work Lieutenant," replied the Zygon commander, "put him in a holding cell."

"Acknowledged," answered the Lieutenant

"With the Time lord confined, we shall have no difficulty in subjugating this planet," the commander soliloquized.

"Uhg, this traffic," Annie said "At this rate, I could get to the lake faster by walking."

"Working on a solution," K-9 buzzed.

A few moments later the traffic signal turned green.

"Finally," Annie huffed, "Now if only we could make this light."

"Affirmative. I sent a signal to the traffic control devices to allow us to pass as we approach."

"Well that is very helpful. Good work, K-9."

The Doctor woke to the sight of a small, earthy room with a greenish light shrouding the walls. The room was a small confinement cell on a Zygon starship.

"So Time lord," said the Zygon commander standing in the center of the room, "It seems you have discovered our operation here."

"So it seems," the Doctor replied as he began to stand up, "May I ask what your operation here is?"

"Since you are confined and unable to interfere, Doctor, I will tell you some of our mission. There are dozens of ships hidden throughout this planet. Each one contains a Zygon crew that will infiltrate powerful corporations run by humans then complot to take over this planet," the commander said proudly.

"I see. World domination. Is that all? And what about the humans? Do you plan on making them your servants?"

"We will greatly reduce the human population to make room for the new Zygon empire."

"Ever thought of living alongside humans, in disguise of course. I don't think humans are quite ready to accept non-terrestrial beings living amongst them."

"Disgraceful! A Zygon should never have to live like those primitives. We are a superior species; we shall have the right to take over this world and make it our own. I would expect you, Doctor, to understand that considering the Time Lords are more advanced than the primitives of this world."

"Commander," a voice interrupted.

"What is it, lieutenant?"

"A primitive has been detected outside the concealed entrance," the lieutenant stated.

"A human outside our hidden entrance does not concern me. After all it will not be able to find the door very easily. At any rate, I have other matters to attend to," with that, the Commander left the cell and locked the Doctor inside.

"Good day to you too," he muttered as he searched his pockets for his sonic screwdriver.


	4. Chapter 4

Annie and K-9 arrived at Lake Apopka and discovered that the area was extremely quiet.

"Ok K-9, we're here," Annie stated as she bent down to pick up a large stick on the ground. "Can you determine where the ship's entrance is located?" _I can't believe how quiet it is._

"The exterior entrance is located approximately 91.44 meters southwest."

"Thanks K-9."

After a couple of minutes of walking, Annie noticed an unusual tree with a curious appearance. "Hello, what's this?" she asked aloud. "This is a very strange looking tree." The tree seemed like any other tree except for the trunk. The trunk was almost perfectly cylindrical and wide enough for three people to fit inside. After a careful look, Annie realized that it might be an entrance to the Zygon ship. "You know K-9, I think this might be the entrance, but I don't see any mechanism that would open the door. Hold on, there is what appears to be a button over here to the side." She pushed the button thereupon opening the door; she peered inside then turned to K-9. "Well, here we go."

* * *

"Commander."

"Yes, Lieutenant?"

"The primitive has found a way inside the entrance."

"It seems I have underestimated the humans. Lieutenant, go find this human and bring it to me alive."

"Yes Commander."

"This is rare. A human should not have been able to find the entry through the perception filter. There is something unique operating here," he said to himself.

* * *

After Annie and K-9 entered the door, they discovered a tunnel that led directly to the Zygon ship. "Alright K-9, be on your guard for any living thing."

"Initiating scan for living organisms," K-9 said in response.

"Good. Now let's keep quiet and look for Mr. Anderson and the Doctor."

They silently passed through the tunnel, pausing when they heard the slightest sound. The passage was dark except for an eerie green light that veiled the tunnel. After several harrowing minutes, they arrived at more luminous junction where the tunnel split into four more paths.

"Two lifeforms approaching. One directly ahead and another from far right tunnel," alerted K-9.

Annie pulled out a lighter from her pocket in hope that the fire from the lighter would scare the Zygons and readied the branch in her hand to attack whatever came through the tunnels in case the lighter failed to scare off the Zygons or something else came through.

"Annie?" said a voice from the passage ahead of them.

"Mr. Anderson? Is that you?" she asked.

"Yes. It's me," he said as he stepped into the light.

"It's good to know you're all right," she said with relief. "Have you seen a tall man with a long scarf anywhere around here?"

"Annie," came another voice.

"Doctor?" Annie asked slightly confused. "Good to know you're all right too. I've found Mr. Anderson. We should get out of here before a Zygon finds us."

"Incorrect," K-9 interjected. "Scan suggests that a Zygon is already in this corridor."


	5. Chapter 5

"Where?" she whispered.

"I am unable to ascertain where the Zygon is," responded K-9.

"Some help you are," she mumbled.

Annie activated the lighter and cautiously scanned the corridor. As the lighter produced a flame, Mr. Anderson took a small step back, but the Doctor seemed unaffected.

"We should get out of here," Annie whispered to the group. "This is the way I came in. Let's go this way."

"No," Mr. Anderson interjected, "There is another exit this way, plus this way is safer." he gestured to the corridor behind him.

"But this way leads straight to the exit and I am fairly certain that there are no Zygons down this path."

"I agree with Annie. We should go that way," said the Doctor.

"No, I have been ordered to take you to the Commander," Mr. Anderson hissed as he morphed into a towering, reddish creature covered in suckers.

"Annie! Look out!" the Doctor shouted as the Zygon Lieutenant began to chase her.

The Doctor darted in the direction of the Lieutenant to stop him, but he was repelled. Annie had dropped her stick and lighter and took a few steps back then stumbled when the monster rushed towards her. Then K-9 fired a laser at the Lieutenant stunning him.

"Are you all right?" asked the Doctor as he helped Annie up.

 _He actually changed. Right in front of me. May be everything he said was true._ She thought in disbelief.

"Annie?"

"Yeah, I wasn't expecting him to be a Zygon," Annie sighed.

"Those creatures can be very convincing in their disguises. Come on, let's get out of here before more show up."

"I'm not leaving without Mr. Anderson," she said adamantly, "If a Zygon was able to pose as him, then he must still be alive just as you said earlier."

"Fine. Let's go find your boss."

Annie collected her stick and lighter then followed the Doctor and K-9 through one of the corridors. The passage was identical to the one that Annie and K-9 entered into earlier; this time they were very vigilant for anything thing could emerge from the dark.

It seemed like hours had passed when the trio had reached a slightly brighter room. Luckily for them, they did not encounter any Zygons along the way. The room they entered had what appeared to be a control board with organic looking instruments. A few corridors also opened towards the room.

"We must be on the bridge," the Doctor whispered.

"Indeed you are," came a voice from the dark. "I am impressed with you, Doctor and human. You were able to escape your cell, Time lord, and you, human, were able to find the entrance to my ship despite the perception filter."

"Perception filter? Show yourself!" Annie said as she ignited the lighter.

"I must congratulate you two," said the voice as he stepped into the light, "However, I must know how you, human, got past the perception filter. It should have encouraged creatures to stay away from the area and much more, conceal the entrance to my ship."

"I didn't realize there was a perception filter thingy that was supposed to keep me away."

"How did you get past it?"

"I don't know. Who are you anyway and where are you holding Mr. Anderson."

"Commander," came another voice from a corridor, "The Time lord has…" the owner of the new voice paused and became fearful as he saw what was in Annie's hand. "A flame… the girl has a flame." The startled Zygon darted back through the hallway from which he came. Seeing the reaction, Annie increased the blaze of the lighter hoping to scare the commander away.

"Are you trying to scare me with that little flame, girl? You're going to need something bigger to frighten me," the commander then began to run toward Annie. She readied the stick in her hand then jumped out of the way as he got closer. She whacked the commander in the back of the head as hard as she could rendering him unconscious.

"Big enough for you?"

"Did you need to hit him?" the Doctor asked. "Nevermind that, I've found where they're holding Mr. Anderson. Come on." With that the they set off to get Mr. Anderson.

"How did you find out where he is?" Annie asked

"While you were conversing with the commander, I searched the computer to learn more about the operation they have here as well as find where they were keeping your boss."

"Well at least it saved us some time, but he was about to attack me, I could have been killed."

"You seemed to handle it fairly well. Here we are."

They stood in front of a booth containing a human figure inside. The Doctor pushed a button which opened the booth revealing Mr. Anderson's sleeping form.

"Mr. Anderson!" Annie exclaimed. "Is he ok?"

"Quite fine. He's in stasis; the Zygons have to keep their subjects in this manner so they can copy them," the Doctor affirmed.

"Is there anything we can do to get him out of this?"

"This should help," The Doctor pulled out his sonic screwdriver and scanned him. Within moments, Mr. Anderson came to.

"Dad! I - I mean Mr. Anderson. Are you all right?" Annie asked.

"Annie?" he said languidly. "I'm fine. Where are we?"

"We are on board a Zygon star ship, and if we don't leave soon we will meet the crew," the Doctor said.

"Zygon star ship?"

"We explain later. Right now we need to get out of here before a Zygon finds us," Annie said authoritatively.

" _Attention all units. Prepare for takeoff,"_ commanded a voice through a speaker.

"Hurry!" the Doctor shouted.


	6. Chapter 6

They darted through the corridors as the ship prepared to take off. They did not run into any of the crew because they were preoccupied with readying the ship. A few moments later the Doctor, Annie, Mr. Anderson, and K-9 were out of the craft and stood in the woods facing the lake. The ground shook and the lake began to rise, then the Zygon starship emerged from the water. It hovered above the disturbed lake then ascended up to the sky.

"I wonder what made them leave," Annie inquired.

"I may have sent them a message from their general telling them to recall all earth units," the Doctor said.

"Will that keep them away?" asked Annie.

"For a while at least. I imagine they may try again in the future," said the Doctor.

"Can someone please explain to me what is going on?" inquired Mr. Anderson.

Annie told her boss everything that happened while he was on the Zygon ship, as they were heading to her car. Once they were heading back to the food bank, Mr. Anderson fell asleep.

"I noticed you called Mr. Anderson "dad" back in the ship," the Doctor said.

"He is my adoptive father. Many years ago he and his wife adopted me from an orphanage in California. When I was old enough, he brought me into the company to work as his secretary."

"So you're an orphan?"

"I'm not sure. I don't remember my birth mother too well; she disappeared when I was a child. This necklace is all I have to remember her by. I wear it in hope that one day I'll find her. Originally she gave it to me as bracelet, but I made it into a necklace so I wouldn't outgrow it. My biological father died not too long after my mom vanished. He never spent much time with me, instead he was almost always working on some sort of vehicle. When he had passed, two federal agents found me and put me in a decent orphanage. A few years later, Mr. Anderson and his wife adopted me. Then we moved here to Florida." There was a brief pause before Annie spoke again. "What's a Time lord?"

"A Time lord is me," the Doctor replied. "Why do you ask?"

"One of the Zygons said something about a Time lord. So what does that mean? Do you own a clock store or something?"

"It means I am a member of a high order of Gallifrey."

"Where's Gallifrey? It sounds like a place in Ireland."

"It's a planet in the constellation of Kasterborous."

"So you're from another planet. Interesting." After that they were silent, but only for a few minutes for they had arrived at the food bank.

* * *

"Thank you, Doctor," Mr. Anderson said as they walked towards the offices. "If it's anything like Annie said, you just saved the whole world."

"Well, it would not be the first time," The Doctor stated. Mr. Anderson gave him a confused look. "I must be off." he continued as he held out a small sack to Annie and Mr. Anderson, "Would you like a jelly baby?"

* * *

"So Doctor, what will you do now that the Zygons are gone?" Annie asked as she accompanied him out the building.

"Oh I'll continue traveling with K-9; exploring the universe and things of that sort. How about you?"

"I'll go back to work and search for something to do with my life."

"Would you like to travel with me?"

"That sounds fun, but I would have to clear it with Mr. Anderson first."

"My ship is a time machine. I can bring you back before anyone ever notices you're gone. I can also help you find your mother."

Annie's eyes widened and began to sparkle with hope. "All right I'll go with you."

The Doctor smiled then led Annie to the Tardis which was parked surprisingly close by.

"That's your ship? But it's a tiny old phone box," Annie pointed out.

"Looks can be deceiving. You should know that," The Doctor retorted while unlocking the phone box. He stepped aside, "Have a look inside." and gestured towards the interior.

Annie approached the box and poked her head inside. Her jaw dropped as she gawked at the interior of the ship. She slowly walked inside and took in everything she saw. The interior was white with round designs on the walls, in the center there was a control board somewhat similar to the board in the Zygon ship, there was also a corridor which seemed to lead to other rooms. There was also a lite hum that resonated throughout the ship. To Annie the hum made the ship seem alive.

"Welcome to the Tardis," said the Doctor as he and K-9 followed her in. "My granddaughter came up with that term. It stands for Time and Relative Dimensions in Space."

"This is impossible," Annie stated, "It looks like a small phone box on the outside. How is it bigger on the inside. Hold on, granddaughter?"

"Time lord technology, the interior exists in a different dimension. It's quite remarkable really. And yes, I have a granddaughter, but that's a different story." He paused as he manipulated some controls on the board. "So, where would you like to go first?"

* * *

"So it seems everything is falling into place thus far," said a woman watching the Doctor and his new companion through a screen. The woman wore a red kimono-like blouse with matching red pants and a devilish grin on her face. As she watched the two converse in the safety of the Tardis, a door had opened in her lab. A grey reptilian humanoid entered the room. The woman turned to see who had entered. "Ah, Chonotas, Are you ready for your next task?"

* * *

Thank you all for reading this story. This is my first fan-fiction that I have completed and I do plan on making sequels to this tale. I hope you all enjoyed the story. Reviews would be lovely.

On a side note, any guesses on who the woman is in the very end?

Until next time the next time... Allons-y!


End file.
